get_serial_interval_density: Dataframe with dates and contact symptom begin probability

In smidm: Statistical Modelling for Infectious Disease Management

Dataframe with dates and contact symptom begin probability

Description

Creates a dataframe containing probability that a contact will start showing symptoms (serial interval) at a particular date/time, given the symptom_begin_date.

Usage

get_serial_interval_density(
  symptom_begin_date,
  max_serial_interval_days = 20,
  shape_serial = 2.154631545,
  rate_serial = 0.377343528
)

Arguments

symptom_begin_date	Date, when the index person got symptoms.
max_serial_interval_days	Number of serial interval days.
shape_serial	Number, the shape parameter for the gamma distribution.
rate_serial	Number, the rate parameter for the gamma distribution.

Details

shape_serial and rate_serial are the parameters of the gamma distribution for the serial interval derived from Najafi et al. (2020).

Value

Dataframe with dates and contact symptom begin probability.

References

Najafi F et al. (2020) "Serial interval and time-varying reproduction number estimation for COVID-19 in western Iran.". New Microbes and New Infections, 36: 100715.

Examples

get_serial_interval_density(as.Date("2022-03-22"))
get_serial_interval_density(as.Date("2022-03-22"), max_serial_interval_days = 20,
                            shape_serial = 2.15, rate_serial = 0.38)

smidm documentation built on Aug. 27, 2022, 9:06 a.m.